Bio::EnsEMBL::Collection Gene
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Summary
Bio::EnsEMBL::Collection::Gene - Feature collection implementation
for gene features.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Argument ( ' rearrange ' )
Bio::EnsEMBL::Utils::Exception ( ' throw ' )
Synopsis
No synopsis!
Description
A gene is represented by the basic feature representation (see
documentation of Bio::EnsEMBL::Collection) and by the following extended
feature representation:
    1.
    Display label (display ID of the display Xref), if defined, otherwise
undef.
    2.
    Biotype
    3.
    Status
    4.
    Is-current
    5.
    Stable ID
    6.
    Version
    7.
    Created date
    8.
    Modified date
    9.
    Description
    10.
    Confidence.
    11.
    External name
    12.
    External database name
    13.
    External status
    14.
    Source
Methods
_columns
No description
Code
_create_feature
No description
Code
_create_feature_fast
No description
Code
_default_where_clause
No description
Code
_tables
No description
Code
Methods description
None available.
Methods code
_columnsdescriptionprevnextTop
sub _columns {
  my ($this) = @_;

  my @columns = $this->SUPER::_columns();

  if ( $this->lightweight() ) {
    @columns[ Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns ] =
      map( 1, Bio::EnsEMBL::Collection::BASIC_SLOTS .. $#columns );
  }

  return @columns;
}
_create_featuredescriptionprevnextTop
sub _create_feature {
  my ( $this, $feature_type, $args ) = @_;

  my $feature = $this->SUPER::_create_feature( $feature_type, $args );

  if ( !$this->lightweight() ) {
    my ( $stable_id,     $version,     $external_name,
         $type,          $external_db, $external_status,
         $display_xref,  $description, $created_date,
         $modified_date, $confidence,  $biotype,
         $source,        $status,      $is_current )
      = rearrange( [ 'STABLE_ID',     'VERSION',
                     'EXTERNAL_NAME', 'TYPE',
                     'EXTERNAL_DB',   'EXTERNAL_STATUS',
                     'DISPLAY_XREF',  'DESCRIPTION',
                     'CREATED_DATE',  'MODIFIED_DATE',
                     'CONFIDENCE',    'BIOTYPE',
                     'SOURCE',        'STATUS',
                     'IS_CURRENT'
                   ],
                   %{$args} );

    push( @{$feature},
          $display_xref->display_id() || undef, $biotype || $type,
          $status,          $is_current,
          $stable_id,       $version,
          $created_date,    $modified_date,
          $description,     $confidence,
          $external_name,   $external_db,
          $external_status, $source );
  }

  return $feature;
}
_create_feature_fastdescriptionprevnextTop
sub _create_feature_fast {
  my ( $this, $feature_type, $args ) = @_;

  throw(   '_create_feature_fast() '
         . 'is not implemented for '
         . 'gene collections' );
}
_default_where_clausedescriptionprevnextTop
sub _default_where_clause {
  my ($this) = @_;

  if ( $this->lightweight() ) { return '' }

  return $this->SUPER::_default_where_clause();
}

1;

# $Id: Gene.pm,v 1.10 2009/03/04 10:58:13 ak4 Exp $
}
_tablesdescriptionprevnextTop
sub _tables {
  my ($this) = @_;

  my @tables = $this->SUPER::_tables();

  if ( $this->lightweight() ) { return ( $tables[0] ) }

  return @tables;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.